Methods to Determine Conditions of a Hydrocarbon Reservoir

ABSTRACT

A method of identifying in situ conditions of a hydrocarbon reservoir is disclosed. The method comprises, obtaining a sample from an area of interest, such as a sediment sample or water column sample near a hydrocarbon seep; analyzing the sample to detect lipid, protein, and/or nucleic acid signatures that are indicative of the Thermotogales order; identifying the relative abundance of the different genera and/or species of the Thermotogales present in the sample to generate a taxonomy signature of the sample; and then using the taxonomy signature to determine conditions, such as temperature, of the hydrocarbon reservoir.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/357,587 filed Jul. 1, 2016, U.S. Provisional Application No.62/357,595 filed Jul. 1, 2016, and U.S. Provisional Application No.62/357,597 filed Jul. 1, 2016, the entirety of which are incorporatedherein by reference.

FIELD OF THE INVENTION

Described herein are methods for determining in situ conditions of ahydrocarbon reservoir. In particular, the methods utilizemicrobiological data from hydrocarbon seeps to ascertain in situconditions of a hydrocarbon reservoir, such as the temperature of ahydrocarbon reservoir.

BACKGROUND

The exploration for and discovery of new oil reserves has becomeincreasingly challenging and costly. Untapped reserves tend to be moredifficult to identify and evaluate, and are often located subsea, whichfurther increases the complexity and cost of discovering such reserves.Successful, efficient, and cost effective identification and evaluationof hydrocarbon-bearing reservoirs is therefore very desirable.

In marine exploration, seep detection has become an important tool toidentify potential hydrocarbon resources in the subsurface. Oil and gasaccumulations often leak hydrocarbons including methane, ethane,propane, butane, naphthalene, and benzene. These hydrocarbons maymigrate toward the surface (i.e., the seafloor), through a variety ofpathways, such as faults or fracture zones. As such, the seeps becomesurface expressions of subsurface geological phenomena and can be usedto give an indication of the subsurface conditions. In some instances,seeps may not be directly above the accumulation from which theyoriginate but rather have further migrated and mixed with the sea water.

Analysis of fluid and sediment samples that are collected from, in, andaround hydrocarbon seeps can be used to determine the presence of amature source rock. However, such analysis cannot confirm or disprovewhether the hydrocarbon seep is also connected to a hydrocarbonreservoir. That is, in some instances, while the seep is emanating froma source rock, the source rock may not be connected to a hydrocarbonreservoir. As such, there is a desire to for methods that enable one todetermine whether or not a hydrocarbon seep is connected to ahydrocarbon reservoir.

The microbial ecology of a hydrocarbon seep can provide additionalinformation that may be used to characterize the hydrocarbon reservoirfrom which the seep emanated. That is, it may be possible to usebiological information from the hydrocarbon seep for exploration andhydrocarbon characterization purposes. For example, PCT Publication No.WO 2013/119350 describes using the community function and communitystructure of a sample ecology from a hydrocarbon seep to determine thelocation of a hydrocarbon reservoir. Additionally, U.S. PatentApplication Publication No. 2006/0154306 describes using genotypicanalysis of a sample for the presence of thermophilic or extremophilicmicroorganisms and comparing the biological profile of the sample tothose from reference samples to determine the type of oil, quality ofoil, gas/oil ratio, depth, or migration route of the sample. Further,U.S. Pat. No. 8,071,295 describes methods for performing surveys of thegenetic diversity of a population, creating a database comprising thesurvey information, and analyzing the information to correlate thepresence of nucleic acid markers with desired parameters in a sample,where the surveys are useful in the fields of geochemical exploration,agriculture, bioremediation, environmental analysis, clinicalmicrobiology, forensic science, and medicine.

However, much of the work used to obtain biological information fromhydrocarbon systems has relied on culture-based techniques. Thesetechniques are limited because many of the organisms, particularly thoseliving within a hydrocarbon reservoir, are not able to be cultured.While identifying and finding microbes that have originated in thereservoir and have been transported to the surface would be ideal, it islikely that only a limited number of the microbes would possibly survivetransport intact. Thus, relying on culture-based techniques may not befeasible or provide a full representation of the subsurfacebiodiversity.

In addition, past studies have assumed that organisms living in thesubsurface are similar to those at the surface. However, recent evidenceindicates that the biodiversity in the subsurface is quite complex andmany the subsurface species found have not been identified previously.Thus, with increasing genetic divergence from known reference species,the use of “lab-on-a-chip” type tools (e.g., microarrays usingoligonucleotide-type probes or polymerase chain reaction (PCR) methods)that require specific binding of probes to identify certain known targetbiological species becomes less effective. That is, many of theprobe-based methods may be restricted to finding organisms that havesome genetic similarity to known organisms, and therefore canpotentially fail to identify a large portion of the species within asample.

Application of microbiology-based tracers has also been used to identifywhether thermogenic hydrocarbons are present, by examining wherehydrocarbon degradation occurs or is associated with known functionssuch as bacterial sulfate reduction or reactions that alter fluidproperties. However, while these methods are useful for identifyingdiagnostic organisms or probes associated with a particular function,they do not provide information about the in situ conditions, such asthe pressure, temperature, or salinity, within the reservoir.

Therefore, it would be desirable to have improved methods of usingbiological information from the hydrocarbon seep for exploration andhydrocarbon characterization purposes. For example, there is a need forimproved methods for determining whether a hydrocarbon seep is connectedto a hydrocarbon reservoir and for methods to characterize thehydrocarbon reservoir from which the seep emanated. For example, thereis a need for improved methods for determining in situ conditions of ahydrocarbon reservoir, such as determining the temperature of thehydrocarbon reservoir.

Additional background references may include U.S. Patent ApplicationPublication Nos. 2010/279290, 2011/0118983, 2012/0158306, 2013/0157275,2014/0227723, 2014/0315765, and 2015/0291992; PCT ApplicationPublication Nos. WO 2010/109173, WO 2012/016215, WO 2015/103165, and WO2015/103332; GB Patent Application Publication No. 2478511 A; ChinesePatent Application Publication Nos. CN 102154453, CN 104630336, and CN104651350; Lazar et al., “Distribution of anaerobic methane-oxidizingand sulfate-reducing communities in the Gil Nyegga pockmark, NorwegianSea, Vol. 100, No. 4, pp. 639-653 (July 2011); Orphan et al.,“Culture-Dependent and Culture-Independent Characterization of MicrobialAssemblages Associated with High-Temperature Petroleum Reservoirs”,Applied and Environmental Microbiology, Vol. 66, No. 2, pp 700-711(February 2011); and Waldron et al., “Salinity Constraints on SubsurfaceArchaeal Diversity and Methanogenesis in Sedimentary Rock Rich inOrganic Matter”, Applied and Environmental Microbiology, Vol. 73, No.13, pp 4171-4179 (July 2007).

SUMMARY

Described herein are methods for determining conditions, such as thetemperature, of a hydrocarbon reservoir. The methods described hereinanalyze the microbial community found in a hydrocarbon seep to identifywhether the hydrocarbon seep is connected to a hydrocarbon reservoir andto determine properties of the hydrocarbon reservoir.

The methods may comprise obtaining one or more samples near ahydrocarbon seep. For example, the sample may be obtained within aradius of 150 meters, or 125 meters, or 100 meters, or 75 meters, or 50meters, or 25 meters, or 20 meters, or 15 meters, or 10 meters, or 5meters, or 3 meters, or 1 meter from the center of the location wherethe seep is emanating from the seafloor. The sample may be a fluidsample from the water column or a sediment sample from the sea floor.

The sample may be processed to extract the nucleic acids from thesample. The extracted nucleic acids may then be amplified and/orsequenced. The amplified/sequenced nucleic acids are then analyzed toidentify genetic markers and/or signatures that are indicative of thepresence of one or more microorganisms from the order Thermotogales, andin particular the family of Thermotogaceae. The community structure ofthe Thermotogales within the sample may then be analyzed to identifymicroorganisms from one or more of the genera Defluviitoga,Fervidobacterium, Geotoga, Kosmotoga, Marinitoga, Mesotoga, Oceanotoga,Petrotoga, Thermopallium, Thermosipho, and Thermotoga. In particular,the nucleic acid signature may be analyzed to determine the relativeabundance of the genera Thermotoga, Petrotoga, and Kosmotoga within thesample.

The signatures can then be used to identify the signature of thehydrocarbon reservoir. For example, the hydrocarbon reservoir isidentified as having a temperature of less than 60° C. when thecommunity structure of the sample indicates that the sample contains50-100% of microbes from the genera of Petrotoga, Kosmotoga, or amixture thereof. For example, the hydrocarbon reservoir is identified ashaving a temperature of from 60 to 80° C. when the community structureof the sample indicates that the sample contains 40 to 100% of microbesfrom the genera of Thermotoga, less than 30% of microbes from the generaof Petrotoga, and less than 30% of microbes from the genera ofKosmotoga. For example, the hydrocarbon reservoir is identified ashaving a temperature of greater than 80° C. when the community structureof the sample indicates that the sample contains less than 30% ofmicrobes from the genera of Thermotoga, less than 30% of microbes fromthe genera of Petrotoga, less than 30% of microbes from the genera ofKosmotoga, and from 30-100% of the microbes that are Archaea.

In some embodiments, the method may further comprise calibrating thegenetic signature of the sample obtained near the hydrocarbon seep bycomparing the signature to a signature of a sample obtained away fromthe hydrocarbon seep. For example, the method may comprise obtaining areference sample (such as a water column sample or a sediment samplefrom the seafloor) at a location that is radially at least 200 meters,or at least 250 meters, or at least 300 meters, or at least 350 meters,or at least 400 meters, or at least 450 meters, or at least 500 metersaway from the center of the location where the seep is emanating fromthe seafloor. The reference sample may then be subjected to the nucleicacid, lipid, and protein extraction and sequencing to determine thesignature of the reference sample. The signature from the hydrocarbonseep sample may then be calibrated by comparing it to the signature fromthe reference sample.

DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic illustrating a cross section view of a hydrocarbonsystem and an associated seafloor seep.

FIGS. 2A, 2B, 2C, and 2D are schematics illustrating cross section viewsof different types of seafloor hydrocarbon seeps.

FIG. 3 is a block diagram of a workflow according to methodologies andtechniques described herein.

DETAILED DESCRIPTION OF THE DISCLOSURE

To the extent the following description is specific to a particularembodiment or a particular use, this is intended to be illustrative onlyand is not to be construed as limiting the scope of the invention. Onthe contrary, it is intended to cover all alternatives, modifications,and equivalents that may be included within the spirit and scope of theinvention.

Example methods described herein may be better appreciated withreference to flow diagrams. While for purposes of simplicity ofexplanation, the illustrated methodologies are shown and described as aseries of blocks, it is to be appreciated that the methodologies are notlimited by the order of the blocks, as some blocks can occur indifferent orders and/or concurrently with other blocks from that shownand described. Moreover, less than all the illustrated blocks may berequired to implement various embodiments of an example methodology.Blocks may be combined or separated into multiple components.Furthermore, additional and/or alternative methodologies can employadditional blocks not shown herein. While the figures illustrate variousactions occurring serially, it is to be appreciated that various actionscould occur in series, substantially in parallel, and/or atsubstantially different points in time.

Various terms as used herein are defined below. To the extent a termused in a claim is not defined below, it should be given the broadestpossible definition persons in the pertinent art have given that term asreflected in at least one printed publication or issued patent.

“Amplification” is the generation of multiple copies of nucleic acidsegments to enhance the analysis of very low amounts of nucleic acids.For example, amplification may be performed by a polymerase chainreaction (“PCR”), which uses a thermostable polymerase enzyme, such asthe TAQ enzyme for DNA, to exponentially produce thousands or millionsof copies of a DNA segment during a number of thermal cycles. Duringeach cycle, the DNA segments produced in a previous cycle becometemplates for new copies of that segment. RNA analysis may be performedby reverse transcripting the RNA to create cDNA segments, which may thenbe amplified.

As used herein, “behavior” encompasses responses to stimuli. Forexample, the behavior of an organism may indicate the organism'smotility, attachment (including biofilm formation), bioluminescence,mineral precipitation, spore formation, etc.

As used herein, “community composition” refers to the composition of theorganisms in the system. That is, the community composition is anindication of the types or organisms (e.g., bacteria vs. archaea, orspecies x vs. species y) that live or exist in the system.

As used herein, “community structure” refers to the abundance of eachtype of organism in the system. In particular, the community structureis an indication of the relative abundance of the different types oforganisms in the system. For example, the community structure mayindicate that the system comprises 10% bacteria and 90% archaea. In someembodiments, the community structure may look at only a subset of theorganisms within the system and provide an indication of the relativeabundance of certain species within the system as compared to otherspecies within the system. For example, the community structure mayindicate that the system comprises 25% species x, 40% species y, 30%species z, and 5% of unclassified species.

As used herein, “community function” refers to an indication of thetypes of metabolic processes the organisms within the system perform.For example, the community function may indicate that the organismswithin the system are capable of hydrocarbon degradation, sulfatereduction, iron reduction, fermentation, etc.

As used herein, “DNA analysis” refers to any technique used to amplifyand/or sequence DNA contained within the sample. DNA amplification canbe accomplished using PCR techniques or pyrosequencing. DNA analysis mayalso comprise non-targeted, non-PCR based DNA sequencing (e.g.,metagenomics) techniques. As a non-limiting example, DNA analysis mayinclude sequencing the hyper-variable region of the 16S rDNA (ribosomalDNA) and using the sequencing for species identification via DNA.

As used herein, “ecology” refers to the study of the interactionsbetween the living and non-living components of a system. In particular,the ecology of a sample includes information about the biology,microbiology, and molecular biology of components of the sample. Ofparticular reference herein, the ecology of a sample refers to adescription of the organisms that live or exist within a sample, and mayinclude parameters such as community composition, community structure,and community function of the organisms within the sample.

As used herein, “ex situ analysis” refers to the analysis of samplesoutside of their original environment. Culture- or cell-based techniquesrequire that live organisms be captured in order to further study themto make the appropriate assessments are considered ex situ analysis.

The term “field sample” refers to a sample containing material from thenatural environment. Field samples include, but are not limited to,samples taken from any soil (encompassing all soil types and depths),water or liquid (encompassing freshwater aquatic or marine habitats),sediment (encompassing marine sediment, lake or river sediment, or mudsediment), or atmospheric dust or particulates. The field sample mayinclude a multitude of species of microorganisms or a single species ofmicroorganism. In preferred embodiments, the samples are field samplestaken from the sediment or water column near a hydrocarbon seep. In sucha context, the term “near” means the sample is obtained within a radiusof 150 meters, or 125 meters, or 100 meters, or 75 meters, or 50 meters,or 25 meters, or 20 meters, or 15 meters, or 10 meters, or 5 meters, or3 meters, or 1 meter from the center of the location where the seep isemanating from the surface. Reference samples may also be field samplestaken from the sediment or water column away from the hydrocarbon seep.In such a context, the term “away” means the reference sample isobtained at least 200 meters, or at least 250 meters, or at least 300meters, or at least 350 meters, or at least 400 meters, or at least 450meters, or at least 500 meters away from the center of the locationwhere the seep is emanating from the surface, and in some embodiments,less than 2000 meters, or less than 1750 meters, or less than 1500meters, or less than 1250 meters, or less than 1000 meters away from thelocation where the seep is emanating from the surface.

A “geologic model” is a computer-based representation of a subsurfaceearth volume, such as a petroleum reservoir or a depositional basin.Geologic models may take on many different forms. Depending on thecontext, descriptive or static geologic models built for petroleumapplications can be in the form of a 2-D or 3-D array of cells, to whichgeologic and/or geophysical properties such as lithology, porosity,acoustic impedance, permeability, or water saturation are assigned (suchproperties are referred to collectively herein as “reservoirproperties”). Many geologic models are constrained by stratigraphic orstructural surfaces (for example, flooding surfaces, sequenceinterfaces, fluid contacts, and/or faults) and boundaries (for example,facies changes). These surfaces and boundaries define regions within themodel that possibly have different reservoir properties.

As used herein, “genomics” refers to the study of genomes of organisms,which includes the determination of the entire DNA or RNA sequence oforganisms as well as genetic mapping.

A “hydrocarbon” is an organic compound that primarily includes theelements hydrogen and carbon, although nitrogen, sulfur, oxygen, metals,or any number of other elements may also be present in small amounts. Asused herein, hydrocarbons generally refer to organic materials (e.g.,natural gas and liquid petroleum) that are harvested from hydrocarboncontaining sub-surface rock layers, termed reservoirs.

As used herein, “hydrocarbon management” or “managing hydrocarbons”includes hydrocarbon exploration, hydrocarbon extraction, hydrocarbonproduction, identifying potential hydrocarbon resources, identifyingwell locations, determining well injection and/or extraction rates,identifying reservoir connectivity, acquiring, disposing of and/orabandoning hydrocarbon resources, reviewing prior hydrocarbon managementdecisions, and any other hydrocarbon-related acts or activities.

As used herein, “hydrocarbon exploration” refers to any activityassociated with determining the location of hydrocarbons in subsurfaceregions. Hydrocarbon exploration normally refers to any activityconducted to obtain measurements through acquisition of measured dataassociated with the subsurface formation and the associated modeling ofthe data to identify potential locations of hydrocarbon accumulations.Accordingly, hydrocarbon exploration includes acquiring measurementdata, modeling of the measurement data to form subsurface models, anddetermining the likely locations for hydrocarbon reservoirs within thesubsurface. The measurement data may include seismic data, gravity data,magnetic data, electromagnetic data, and the like.

As used herein, “hydrocarbon development” refers to any activityassociated with planning of extraction and/or access to hydrocarbons insubsurface regions. Hydrocarbon development normally refers to anyactivity conducted to plan for access to and/or for production ofhydrocarbons from the subsurface formation and the associated modelingof the data to identify preferred development approaches and methods. Byway of example, hydrocarbon development may include modeling of thesubsurface formation and extraction planning for periods of production,determining and planning equipment to be utilized and techniques to beutilized in extracting the hydrocarbons from the subsurface formation,and the like.

As used herein, “hydrocarbon production” refers to any activityassociated with extracting hydrocarbons from subsurface location, suchas a well or other opening. Hydrocarbon production normally refers toany activity conducted to form the wellbore along with any activity inor on the well after the well is completed. Accordingly, hydrocarbonproduction or extraction includes not only primary hydrocarbonextraction, but also secondary and tertiary production techniques, suchas the injection of gas or liquid for increasing drive pressure,mobilizing the hydrocarbon, or treating the well by, for example,chemicals, or hydraulic fracturing the wellbore to promote increasedflow, well servicing, well logging, and other well and wellboretreatments.

As used herein, “in situ analysis” refers to the analysis of sampleswithin the environment of interest. This approach is similar to othergeochemical measurements, such as pH, temperature, pressure,concentration of dissolved ions, etc., which can be measured using avariety of in situ tools and probes.

As used herein, “lipids” refers to hydrophobic or amphiphilic compoundsthat compose cell membranes of organisms, energy storage, and signalingmolecules.

As used herein, “lipid analysis” refers to quantification and/ordescription of the phospho-lipids present in a sample. Phospho-lipidsare compounds containing two chains of hydrophobic compounds linkedtogether by a hydrophilic head group. Different species of bacteria andarchaea produce different types of lipids. Additionally, all knownbacterial lipids are joined together with an ester bond while all knownarchaeal lipids are joined together with an ether bond. Thus, intactlipids can provide information about the community structure ororganisms in a sample. Further, as lipid production may vary as afunction of temperature, pressure, and/or salinity, lipid analysis mayprovide information about reservoir conditions. While the hydrophilichead group in a lipid is easily degradable, the remaining hydrophobicchains are quite stable. As such, derivatives of these chains can beused as biomarkers in organic geochemistry to fingerprint oils.Unaltered lipids can be used in a similar matter. Altered lipids canalso be used to fingerprint oils in organic geochemistry. Non-intactlipids can provide information about community structure in the past.That is, non-intact lipids can provide information about prior communitystructures that can be used to indicate that conditions in the communitywere different at some point of time in the past. Thus, non-intactlipids can allow one to identify areas of past microbiological activitywhere DNA based markers have already been destroyed.

As used herein, “metabolites” refer to compounds produced by bacteriaand/or archaea during respiration or fermentation. For example, aceticacid is an example of a metabolite. Metabolites can provide informationabout the type of hydrocarbon being used as a substrate as well asinformation about physical and chemical conditions in the reservoirs.For example, the presence of specific metabolites may indicate or inferthe presence of hydrocarbons and/or conditions at depth.

A “microbe” is any microorganism that is of the domain Bacteria,Eukarya, or Archaea. Microbes include bacteria, fungi, nematodes,protazoans, archaebacteria, algae, dinoflagellates, molds,bacteriophages, mycoplasma, viruses, and viroids.

As used herein, a “microarray” is a multiplex lab-on-a-chip that allowsmany tests to be performed simultaneously or in sequence. It is an arrayof hundreds to thousands of spots containing probes (or tags) of varioustypes. Lab-on-a-chip and microfluidics devices allow for the analysis ofsamples using miniaturized laboratory processes, which require smallsample sizes, such as less than 10⁻⁶ L of the sample, or less than 10⁻⁹L of the sample.

The term “nucleic acid” refers to biopolymers used in cells for thetransfer of information. Nucleic acids include deoxyribonucleic acid(“DNA”), which is generally found in a nucleus of a eukaryotic cell, andribonucleic acid (“RNA”), which is generally found in the cytoplasm of aeukaryotic cell. A prokaryotic cell, such as a bacterial or archea cell,does not have a nucleus, and both DNA and RNA may be found in thecytoplasm of the cell. DNA often provides the genetic code for a cell,although a few types of organisms use RNA to carry heritablecharacteristics. RNA is often associated with the synthesis of proteinsfrom genes on the DNA.

As used herein, “products” refer to proteins, lipids, exopolymericsubstances, and other cellular components that organisms produce under agiven set of conditions.

As used herein, “proteomics” refers to the description of proteinsproduced by bacteria and/or archaea. Proteins can be used to describethe function of the most active members of a microbial community.Proteomics can be used to describe community structure, but only if thelinks between individual species and expressed proteins are clearlyunderstood. Proteins can be separated using two dimensionalelectrophoresis. The proteins can then be analyzed using a TOF (time offlight) mass spectrometer coupled to a liquid chromatograph or a MALDI(matrix assisted laser desorption/ionization) unit. Since proteins arenot easily amplified proteomic analysis in natural samples oftenrequires a large amount of biomass to be successful.

As used herein, “RNA analysis” refers to any technique used to amplifyand/or sequence RNA contained within the samples. The same techniquesused to analyze DNA can be used to amplify and sequence RNA. RNA, whichis less stable than DNA is the translation of DNA in response to astimuli. Therefore, RNA analysis may provide a more accurate picture ofthe metabolically active members of the community and may be used toprovide information about the community function of organisms in asample.

A “reservoir” is a subsurface rock formation from which a productionfluid can be produced. The rock formation may include granite, silica,carbonates, clays, and organic matter, such as oil, gas, or coal, amongothers. Reservoirs can vary in size from less than one cubic foot(0.3048 m³) to hundreds of cubic feet (hundreds of cubic meters). Thepermeability of the reservoir rock may provide paths for production andfor hydrocarbons to escape from the reservoir and move to the surface.

A “seep” or “hydrocarbon seep” or “petroleum seep” is a place wherehydrocarbons escape to the surface, normally under low pressure or flow.Seeps may occur above either terrestrial or offshore petroleumreservoirs, but may also occur above subsurface deposits of organicmaterial, for example, as the organic material degrades. Thehydrocarbons may escape from the reservoir or deposit along geologicallayers, or through fractures and fissures in the rock.

As used herein, a “sensor” is a device that detects and measures one ormore physical, chemical, or biological signals.

As used herein, “sequencing” refers to the determination of the exactorder of nucleotide bases in a strand of DNA (deoxyribonucleic acid) orRNA (ribonucleic acid) or the exact order of amino acids residues orpeptides in a protein. For example, nucleic acid sequencing can be doneusing Sanger sequencing or next-generation high-throughput sequencingincluding but not limited to massively parallel pyrosequencing, Illuminasequencing, or SOLiD sequencing, ion semiconductor sequencing. Forexample, amino acid sequencing may be done by mass spectrometry andEdman degradation.

“Substantial” when used in reference to a quantity or amount of amaterial, or a specific characteristic thereof, refers to an amount thatis sufficient to provide an effect that the material or characteristicwas intended to provide. The exact degree of deviation allowable may insome cases depend on the specific context.

As used herein, “transcriptomics” refers to the amplification and/orsequencing of mRNA (messenger RNA), rRNA (ribosomal RNA), and tRNA(transfer RNA). These types of RNA are used to build and synthesizeproteins. Understanding what transcripts are being used allows one tounderstand what proteins are being produced, and thus providesinformation about the community function of organisms in a sample.

As used herein, “paleo-seep” refers to an area that is no longerseeping.

Fluids and sediments collected in and around hydrocarbon seeps can beused to describe the presence of a mature source rock. Further, asdescribed herein, the presence or absence, and relative abundance ofunique microbial species within the sample can provide an indication ofthe in situ conditions of the hydrocarbon reservoir from which the seepemanated. That is, by analyzing the microbial signature of the samplefrom a hydrocarbon seep, one can infer that certain conditions exist inthe subsurface reservoir. In particular, the presence of microbes thecan survive at extreme conditions can be used as a tracer to identifyhydrocarbon seeps connected to reservoirs. Further, information aboutthe community structure and community function of the samples can beused to describe the physical conditions (e.g., temperature andpressure) and chemical conditions (e.g., salinity) of the connectedhydrocarbon reservoir.

FIG. 1 illustrates a hydrocarbon system 100 that includes an organiccarbon bearing source rock 102 that generates and excretes liquid andgaseous hydrocarbons, which migrate through various migration pathways103 into a reservoir 104. The hydrocarbons are trapped in the reservoir104. A sealing interval above the reservoir prevents further hydrocarbonmigration out of the reservoir. However, hydrocarbons can escape fromthe reservoir and migrate toward the surface (shown in FIG. 1 as aseafloor 108) through a variety of pathways, such as faults 110 orfracture zones 111. This hydrocarbon migration can then result in seeps112 discharging hydrocarbons from the seafloor into the water column.Water samples 124 can be taken at or near a suspected seep 112 todetermine the ecology of the associated water column. For example, thesample may be taken within a radius of 150 meters, or 125 meters, or 100meters, or 75 meters, or 50 meters, or 25 meters, or 120 meters, or 15meters, or 10 meters, or 5 meters, or 3 meters, or 1 meter, from thecenter of the location where the seep is emanating from the seafloor108. A suspected seep may be identified a variety of methods, forexample the presence of physical disturbance of the sediment, bubbletrains, microbial mats, and oil slicks or sheens at the sea-airinterface, may all indicate the presence of an active seep. To controlfor microorganisms present in the water that are not associated with aseep, a water sample 116 may also be taken in a region where there areno known seeps. Thus, by comparing the microbial signatures of thesample from the seep 124 and the control sample 116 one can determinewhich organisms have migrated from the subsurface reservoir. Othersamples 118 may also be collected from shallow sediment on the seafloorto determine the ecology of the seafloor 108. Once a likely site for thehydrocarbon accumulation has been established, an exploration well 114can be drilled and one or more core samples 122 can be taken. Likewise,liquid samples may be collected from a production platform 120.Information from the core samples or liquid samples from the productionplatform can be used to verify or calibrate information determined aboutthe subsurface conditions by the methods described herein.

FIGS. 2A to 2D illustrate different types of seafloor hydrocarbon seeps.FIG. 2A is similar to FIG. 1, and shows a seep 202 directly connected toa hydrocarbon reservoir 204 through a fault 206. FIG. 2B shows a seriesof seeps 208 a, 208 b, 208 c that are indirectly connected to anhydrocarbon reservoir 210 through a series of faults 212 a, 212 b, 212c, 212 d. FIG. 2C shows a pair of seeps 214, 216, independent of anyfaults that are linked to an actively generating source rock 218 inwhich there is no reservoir. FIG. 2D shows a fault-independent seep 220associated with a hydrocarbon reservoir 222. In FIG. 2D, thehydrocarbons in the reservoir 222 overcome the capillary entry pressureof the overlying rock 224 and escape to the surface. As seen in FIGS. 2Ato 2D, hydrocarbon seeps can have vastly different physical conditions,such as being connected to a hydrocarbon reservoir in FIGS. 2A, 2B, and2D versus being independent of a reservoir as seen in FIG. 2C. Further,the hydrocarbon seep can directly emanating from the reservoir as inFIG. 2D, emanate from a fault connected to the reservoir as in FIG. 2A,or emanate from faults that are indirectly connected to a reservoir asin FIG. 2B. The methods and techniques described herein can be used toanalyze the microbial signatures of samples taken from the hydrocarbonseep to identify physical and chemical conditions unique to each system,and thus give an indication of what kind of source the hydrocarbons inthe seep have emanated from.

Physical and chemical conditions in hydrocarbon reservoirs are typicallyvery different from conditions at the seafloor. Pressure and temperatureare both generally higher in hydrocarbon reservoirs than at theseafloor. Additionally, salinity is often higher in hydrocarbonreservoirs than at the seafloor and organic carbon is more abundant in ahydrocarbon reservoir. These differences create different environmentsfor different types of microorganism to thrive in where they otherwisewould not. For example, thermophilic and halophilic bacteria have beenidentified and isolated from hydrocarbon reservoirs that would notnormally exist at the seafloor. As these microorganisms are transportedto the surface via a hydrocarbon seep they can be detected in samplesfrom the hydrocarbon seep. Furthermore, organisms living at reservoirconditions and/or those that are transported to the seafloor expressdifferent proteins and lipids, thereby permitting a determination ofreservoir pressure and temperature based on these variables. In theabsence of an active hydrocarbon system, the links between the watercolumn, seafloor sediment and subsurface ecology become less clear.

Furthermore, the relative contribution of reservoir ecology to the watercolumn, seafloor sediment, and subsurface rock ecology can be linked tohydrocarbon migration pathways and therefore hydrocarbon system type canbe inferred. Samples at seeps that are fed by hydrocarbon reservoirswill share some characteristics with samples taken directly from thosereservoirs. The techniques described herein can be combined withphysical and chemical measurements to create a complete, coherentdescription of the ecology of a given sample, and thus with thehydrocarbon reservoir. That is, samples from hydrocarbon seeps that arephysically connected to a hydrocarbon reservoir will share ecologicalcharacteristics. For example, a sediment sample from a seep will shareecological characteristics with the reservoir where the seeping fluidsoriginated. According to methodologies and techniques described herein,a method is provided explaining how to describe the ecology of a sampleand how to relate the ecology of physically disparate samples tophysiochemical conditions associated with sample, and thus with thehydrocarbon reservoir.

For example, detailed descriptions of sample ecology will highlightdifferences in indicator species, and differences in transcripts,lipids, proteins and metabolites can distinguish seeps connected tolarger hydrocarbon reservoirs from seeps in which no reservoirs arepresent.

Organisms contained in samples are characterized for various phenotypesand physiological aspects. For example, the organisms can be culturedand tested for their ability to survive and grow under a variety ofenvironmental conditions such as pressure, temperature, salinity, etc.The ability of organisms to degrade hydrocarbons of interest may also bedetermined. Organisms exhibiting target characteristics are alsoisolated and characterized at depth. Molecular characterizationtypically requires the extraction of components from samples. Thesecomponents include nucleic acids (e.g., DNA and RNA), proteins, lipids,exopolymeric substances, etc. Analysis of these components requiresvarious techniques which include nucleic acid sequencing, proteinsequencing, and/or some sort of separation and/or hybridization.

The methods and techniques described herein can be used to identifymembers of the order Thermotogale that are unique to hydrocarbonreservoirs with in situ temperatures that range from 40 to 98° C. Thesehydrocarbon reservoirs may also be characterized with pressures as highas 65 MPa and total dissolved solids concentrations as high as 24%.Thermotogale are known thermophiles and hyperthermopiles, and asdescribed herein it has been found that individual genera and species ofthe Thermotogale order have distinct optimal growth temperatures. Thus,the community structure of the Thermotogale present in a sample (i.e.,the relative abundance of different genera and species of theThermotogale present in a sample) can be used to identify thetemperature of the hydrocarbon reservoir. In particular, the detectionof the different genera of Thermotogale can be achieved through nucleicacid sequencing from mixed community DNA using Tehrmotogale specific DNAprobes for fluouresence tagging or DNA primers for PCR. Detection ofunique proteins using antibodies specific to LPS or proteins of theThermotogales, or detection of unique membrane lipids, such as diabolicacids, or other lipid derivatives found only in the Thermotogales usingvarious chromatographic methods such as HPLC or LC/MS can be used. Assuch, the relative abundance of the various Thermotogales present in thesample can be used as indicators of not only the presence of areservoir, but also the physical condition (e.g., temperature) of thereservoir.

For example, for the different genera of the Thermotogaceae family, ifthe community structure of the sample indicates that 50-100% of thefamily is represented by either Petrotoga or Kosmotoga, or a mixturethereof, and less than 30% is represented by a concentration of thegenus Thermotoga, this indicates that the reservoir has a temperature ofless than 60° C. However, if 40 to 100% of the sample is represented byThermotoga, with both Petrotoga and Kosmotoga being represented by lessthan 30% each, this indicates that the hydrocarbon reservoir has atemperature of from 60 to 80° C. Ultra high temperature reservoirs,e.g., those with a temperature of greater than 80° C., are representedby community structures where Thermotoga represent less than 30% of thecommunity, Kosmotoga represent less than 30% of the community, Perotogarepresent less than 30% of the community, and from 30-100% of thecommunity include thermophilic and hyperthermophilic Archaea.

According to aspects of disclosed methodologies, a method is providedfor using the ecology of a sample from a hydrocarbon seep to determinecharacteristics of the subsurface hydrocarbon system. An illustratedmethod is provided with reference to FIG. 3. At block 302 a sample iscollected from the sediment near a hydrocarbon seep or the water columnassociated with a hydrocarbon seep. The samples may be collected by handor by using a remotely operated vehicle. Sediment samples may come fromsmall sediments coops, push cores, box cores, gravity cores, pistoncores, or jumbo piston cores. Liquid samples from the water column mayinclude water and hydrocarbon independently or in a mixture. The samplemay be taken within a radius of 150 meters, or 125 meters, or 100meters, or 75 meters, or 50 meters, or 25 meters, or 20 meters, or 15meters, or 10 meters, or 5 meters, or 3 meters, or 1 meter, from thecenter of the location where the seep is emanating from the seafloor.

If the samples are not being analyzed immediately, the samples may befrozen as soon as possible after collection to preserve the integrity ofthe sample ecology. That is, the sediment, water, and rock/or samplesmay be frozen as soon after collection as possible to prevent organismalchanges within the samples due to the sample being maintained at adifferent conditions than those at which the sample were collected. Forexample, the samples may be maintained at a low temperature, such asless than −60° C., or less than −70° C., or less than −80° C., untilanalyses are performed. In some embodiments, the sample may bemaintained at a temperature in the range of −60° C. to −100° C., or from−60° C. to −80° C., until analyses are performed. For samples that arebeing analyzed in situ, freezing of the samples may not be required.

Once the samples are collected at block 302, the samples are analyzedusing various methods to ascertain aspects of the ecology of the sample.For example, the samples may undergo DNA analysis, RNA analysis,metagenomics (including pyrosequencing), proteomics, transcriptomics,lipid analysis, phenotyping, metabolite analysis, organic geochemistry,and inorganic geochemistry analysis. Thus, at block 304 biologicalmaterial is extracted from the sample. For example, nucleic acids (e.g.,DNA and RNA), proteins, and lipids are extracted from the sample. Lipidsand proteins can be extracted from the sample and purified using knowntechniques. For example, the lipids and proteins can be separated fromthe sample using two dimensional electrophoresis or standardprecipitation techniques. The nucleic acids can be extracted from thesample using known techniques. For example, nucleic acids can beextracted from a sediment sample using a sediment DNA extractiontechnique, such as the MoBio Power Soil DNA extraction kit, or utilizingthe method described in U.S. patent application Ser. No. 15/600,161, thedisclosure of which is incorporated herein by reference.

At block 306 the extracted lipids are analyzed. For example, the lipidscan be analyzed using a high performance liquid chromatography, gaschromatography, and/or mass spectrometer. In particular, the analysis atblock 306 is looking to identity diabolic acids that are present in thesample.

At block 308 the extracted proteins are analyzed. For example, theproteins can be analyzed using a shotgun proteomics or protein probemethods. For example, the proteins can be analyzed using a TOF (time offlight) mass spectrometer coupled to a liquid chromatograph or a MALDI(matrix assisted laser desorption/ionization) unit. In some embodiments,the protein samples can be analyzed as mixed sample. In otherembodiments, the protein samples can be treated with Thermotogalespecific antibodies and visualized with fluorescence or other means ofprotein staining.

At block 310 the extracted nucleic acids are analyzed. For example, theextracted nucleic acids can be sequenced, can be identified by fragmentsize, or can be analyzed using specific DNA/RNA probes. In someembodiments, the nucleic acids can be amplified using specific DNAprobes and then be compared to sequencing libraries such as IlluminaMiSeq/HiSeq, or with versions of ABllon Torrent. In some embodiments,whole cells can be stained with RNA specific probes that are attached toa fluorophore, or detection of the fluorophore can be conducted using aconfocoal or fluorescent microscope.

At block 312, the information from the extracted lipids, proteins,and/or nucleic acids can be used to detect ecology signatures specificto the Thermotogales order. This extracted information is then used atblock 314 to assign taxonomy signatures to the sample identifyingfamily, genus, and/or species of specific Thermotogales present in thesample. The family, genus, and species specific lipids and proteins canbe identified by comparing the community lipids and proteins to knownstandards. Thermotogale specific DNA sequences can be identified using abioinformatics pipeline to assign taxonomy to community samples (withexemplary pipelines being MOTHUR and QIIME) and using a standardsequence database (for example, SILVA, NCBI, GreenGenes) to determinewhich, if any, Thermotogale genera are represented in the sample. Forspecific DNA probes, the presence of an amplicon and then the specificsequence of the amplicon can be compared to known Thermotogale sequencesto identify the specific genus and/or species of Thermotogale present.For the fluorescent probes, any fluorescence would indicate that a matchwas found by the probe, and thus, indicate the presence of the specificgenus or species of Thermotogale being probed for.

The relative abundance of the Thermotogale present in the sample canthen be used to predict the temperature of the hydrocarbon reservoir atblock 316. The order Thermotogales consists of the familyThermotogaceae, which consists of the genera Defluviitoga,Fervidobacterium, Geotoga, Kosmotoga, Marinitoga, Mesotoga, Oceanotoga,Petrotoga, Thermopalliu, Thermosipho, and Thermotoga. The relativeabundance of different genera can be used to indicate the temperature ofthe hydrocarbon reservoir. For example, communities in which Petrotogaand Kosmotoga are most abundant and favored occur at temperatures ofless than 60° C., while communities in which Thermotogoa are mostabundant and favored are at temperatures of 60 to 80° C., andcommunities where Archaea are favored and most abundant are attemperatures greater than 80° C. Thus, if 50-100% of the communitycomprises Petrotoga, Kosmotoga, or a mixture thereof, the hydrocarbonreservoir is indicated to have a temperature of less than 60° C., forexample a temperature in the range of 40 to 60° C. If greater than 30%of the community comprises Thermotoga, less than 30% of the communitycomprises Petrotoga, and less than 30% of the community comprisesKosmotoga, the hydrocarbon reservoir is indicated to have a temperatureof from 60 to 80° C. If the community comprises from 30 to 100% ofArchaea, and less than 30% of Thermotoga, less than 30% of Petrotoga,and less than 30% Kosmotoga, then the hydrocarbon reservoir is indicatedto have a temperature of greater than 80° C., such as from 80 to 100° C.

In some embodiments, the community structure of the samples from thehydrocarbon seep can be compared to the community structure of referencesamples that are not from hydrocarbon seeps. Thus, it can be verifiedthat the marker abundance in the samples from the seep is greater thanthe abundance in reference samples. If the markers are present andsufficiently abundant then the markers can be used to indicate that thesample did in fact come from a hydrocarbon seep and provide informationabout the conditions of the hydrocarbon reservoir. For example, areference sample may be obtained at a location that is at least 200meters, or at least 250 meters, or at least 300 meters, or at least 350meters, or at least 400 meters, or at least 450 meters, or at least 500meters away from the center of the location where the seep is emanatingfrom the surface, and in some embodiments, less than 2000 meters, orless than 1750 meters, or less than 1500 meters, or less than 1250meters, or less than 1000 meters away from the location where the seepis emanating from the surface.

The hydrocarbon reservoir properties that are identified using thetaxonomic signature of the Thermotogales present in the sample that isidentified with reference to FIG. 3, can be used in conjunction orrefined with other information about the community function of thesample. For example, in the sediments and fluids surrounding a coldmethane seep the following microorganisms might be found:Desulfobacterium anilini, Desulfovibrio gabonensis, Archaeoglobusfulgidus Methanobacterium ivanovii, ANME-1 (anaerobic methanotroph), andANME-2. These are organism have common metabolic activities, and have acommunity function of reducing sulfate, oxidizing methane to CO₂, andreducing CO₂ back to methane. This information can then be used to inferother properties about the ecology of the hydrocarbon reservoir, such assalinity or pressure. Note that community structure does not necessarilyimply knowledge about the community function. Likewise, geochemical orgenetic information about a community function does not necessarilyimply the presence or absence of specific species (i.e., communitystructure).

The determination of the community structure and the community functioncan thus be used, together with observing organism behavior interaction,measured physical and chemical conditions, and measured biologicalcomponents and products, to derive and understand the ecology of thesamples. The sample ecology may then be used to determine properties ofthe associated hydrocarbon reservoir. That is, as the sample ecology mayvary depending on pressure, temperature, hydrocarbon type, and volume,the sample ecology may assist in determining pressures, temperatures,hydrocarbon type, and volumes associated with the sample and/or anassociated reservoir.

In an aspect of the disclosed methodologies and techniques, a fluidsample is collected from a reservoir with known physical and chemicalconditions. The ecology of this sample is described using the techniquesdefined herein. A sediment sample is collected from a hydrocarbon seepconnected to the known reservoir. The ecology of this seep is describedin the same manner. Key species are identified via their DNA, RNA andlipids that link the two samples together. Additionally key communityfunctions are identified via proteins, transcripts and metabolites thatrelate the two environments to each other. These links can be used inexploration settings where the links between seeps and reservoirs areless definitive.

The indicators developed herein can be used to identify seeps that arelikely linked to reservoirs. Seeps that are fed from shallow deposits ordirectly from the source rock will not have the same set ofcharacteristics. Additionally, ecology in seafloor sediments can be usedto identify smaller seeps that do not have physical surface expressions.

Paleo-seeps can be identified via intact lipids and metabolites insediments. These compounds are stable enough to remain in the sedimentfor years after active seeping has ceased. Lipid derived compounds arecommonly used to fingerprint oils in organic geochemistry. Thesecompounds are stable over geologic time scales. Paleo-seeps may beassociated with economic hydrocarbon reservoirs that are no longerreceiving new charge from the source rocks.

In addition to conventional exploration, the methodologies describedherein can also provide critical information during unconventionalhydrocarbon exploration and development. Specifically, oil shale, shalegas and oil sand systems have properties that vary as a function oftemperature, pressure, hydrocarbon type, inorganic mineralogy andchemistry. These properties can impact the predicted economic volumesthat can be obtained from these unconventional reservoirs. Oil shale andshale gas are settings where the source rock is the reservoir, whichmeans hydrocarbon migration is limited. Microbial products andbiomarkers may help identify in situ pressures, temperatures andvariations in hydrocarbon types across a geologic area of interest.Although this data would be obtained from test well samples, there isstill an opportunity to calibrate basin and petroleum system models andconstrain fluid or gas properties to better identify and extractresources. The role of indigenous microbial communities in controllingor altering the interface between mineral-hydrocarbon-aqueous phases mayapply for the oil shale scenario, but are perhaps even more critical foroil sands. Typically, added microbial or fungal byproduct slurries areused to help alter subsurface conditions. This alteration isaccomplished by the formation or addition of surfactants or by changingthe hydrocarbon properties or composition. For example, convertingviscous hydrocarbons to methane can help facilitate hydrocarbonextraction. The methodologies and techniques described herein may helpoptimize selection of zones, facies, or formations that have indigenouscommunities that may already produce or enhance hydrocarbon extractionwithout additional treatments. Specifically in oil sands, samples frommultiple zones are combined to produce an aggregate that is thenprocessed to remove the oil. If the proportions of these differentmaterials are adjusted to include those that have increased naturalsurfactants, then this may increase the overall yield obtained from thehomogenized aggregate.

If this data is tied to multiple other parameters that are indicative ofpressure, temperature or salinity in the subsurface, then a more robustassessment may be made. Information about the reservoir, and thehydrocarbon system in general, may be missed by not incorporating orintegrating other geological, geochemical and ecological informationinto traditional or currently existing workflows. This integratedapproach is one option for which the methodologies described herein maybe applied.

As a particular example, ascertaining that a particular hydrocarbon seepis connected to a subsurface hydrocarbon reservoir is an important pieceof information that can be used to reduce the risks associated withexploring for oil and gas. That is, knowing that a hydrocarbon reservoirexists at a certain range of temperatures, pressures, and/or salinitiesnarrows the region in which additional data must be collected beforedrilling a well. That is, the methodologies described herein allow oneto focus exploration efforts on relevant depth intervals and/ordepositional settings, and can ultimately affect ones decision on if,when, and where to drill an exploration well. For example, if it isfound that a hydrocarbon seep is connected to a reservoir that has atemperature of less than 60° C., or from 60 and 80° C., or from 80° C.to 105° C., this temperature range can be converted to a reservoir depthusing the geothermal gradient for the basin. Seismic survey can then bespecifically designed and optimized for targeting that depth range,which can be reduce the overall cost of the survey.

Although the disclosed methodologies and techniques may be appliedadvantageously to oil and gas exploration activities, there are otherways in which said methodologies and techniques may be used, such asmicrobially enhanced oil recovery due to production of methane viamethanogenesis, exopolysaccharides and enzymes causing changes fluidproperties (e.g., viscosity), addition of microbial slurries toenzyme-activated proppants, and surfactants that change the interfacebetween the hydrocarbons and minerals (e.g., emulsion breakers),reducing waxy components and increasing flow. In some cases the need toobtain microbial information is related to the potential for scaleformation, reservoir souring, and pipeline corrosion if left untreated.Although reservoir fluid flow applications are based primarily onintroducing biological tags downhole, critical information about howthese biotechnology systems work may provide necessary insight intofacies-specific properties and behavior, such as zones with uniqueindigenous ecology. From this type of data set, there is potential totarget specific subsurface conditions or intervals and thereforeoptimize site selection based on a particular suite of desiredproperties. In all of these examples, a toolkit that appropriatelyidentifies inherent and diagnostic information linked to ecologic andgeochemical conditions in the subsurface will be helpful to de-risk somezones considered for exploring unconventional hydrocarbon plays orsystems.

The disclosed methodologies and techniques provide a method thatcombines a full suite of geochemical and biological tools to identifyorganisms, their by-products, metabolites and the like that may betransported from the reservoir to the air-sediment or water-sedimentinterface with the fluids and hydrocarbons. This also includesdifferentiation of organisms living in association with thehydrocarbons, or related transported materials, at the interface thatmay shed light on hydrocarbon quality or changes therein due totransport and any degradation that may occur along the migrationpathway. If extracellular DNA and other biomarkers are released withinthe reservoir, there is time for equilibration, reaction and associationwith reservoir geochemistry that may provide characteristic compositionsthat are retained during transport to surface and therefore providesmore opportunity for assessing subsurface conditions. For example, thedisclosed methodologies and techniques that combine metagenomicanalysis, proteomics, lipid analysis, molecular geochemistry, biomarkerand/or isotopic information will provide more information about thereservoir, ecology, and hydrocarbons and fluids therein than could beacquired from other approaches, such as PCR, quantitative PCR (qPCR),microarray or culturing methods alone.

1. A method of determining one or more conditions of a hydrocarbonreservoir comprising: (a) obtaining a sample near hydrocarbon seepassociated with the hydrocarbon reservoir; (b) extracting one or more ofproteins, lipids, or nucleic acids from the sample; (c) analyzing theextracted proteins, lipids, or nucleic acids to identify signatures thatare indicative of organisms from the Thermotogales order; (d)identifying the relative abundance of different genera or species ofThermotogales present in the sample and assigning a taxonomy signatureto the sample; (e) using the taxonomy signature to determine thetemperature of the hydrocarbon reservoir.
 2. The method of claim 1,wherein the hydrocarbon seep is a subsea seep.
 3. The method of claim 2,wherein the sample is obtained from the water column near thehydrocarbon seep.
 4. The method of claim 1, wherein the sample is asediment sample obtained from the seafloor near the hydrocarbon seep. 5.The method of claim 1, wherein the sample is obtained from a locationthat is within a radius of 10 meters from the center of the locationwhere the seep is emanating from the surface.
 6. The method of claim 1,wherein the sample is obtained from a location that is within a radiusof 3 meters from the center of the location where the seep is emanatingfrom the surface.
 7. The method of claim 1, further comprisingpreserving the obtained sample at a temperature at or less than −60° C.until the sample is ready to have the one or more proteins, lipids, ornucleic acids extracted.
 8. The method of claim 1, wherein the samplesare analyzed to identify nucleic acid signatures that are indicative oforganisms from the family Thermotogaceae.
 9. The method of claim 1,wherein the samples are analyzed to identify nucleic acid signaturesthat are indicative of organisms from the genera Defluviitoga,Fervidobacterium, Geotoga, Kosmotoga, Marinitoga, Mesotoga, Oceanotoga,Petrotoga, Thermopalliu, Thermosipho, and Thermotoga.
 10. The method ofclaim 1, wherein the samples are analyzed to identify nucleic acidsignatures that are indicative of organisms from the genera Petrotoga,Kosmotoga, and Thermotoga.
 11. The method of claim 1, wherein thehydrocarbon reservoir is identified as having a temperature of less than60° C. when the taxonomy signature of the sample indicates that thesample contains 50-100% of microbes from the genera of Petrotoga,Kosmotoga, or a mixture thereof.
 12. The method of claim 1, wherein thehydrocarbon reservoir is identified as having a temperature of from 60°C. to 80° C. when the taxonomy signature of the sample indicates thatthe sample contains 40 to 100% of microbes from the genera ofThermotoga, less than 30% of microbes from the genera of Petrotoga, andless than 30% of microbes from the genera of Kosmotoga.
 13. The methodof claim 1, wherein the hydrocarbon reservoir is identified as having atemperature of greater than 80° C. when the taxonomy signature of thesample indicates that the sample contains less than 30% of microbes fromthe genera of Thermotoga, less than 30% of microbes from the genera ofPetrotoga, less than 30% of microbes from the genera of Kosmotoga, andfrom 30-100% of the microbes that are Archaea.
 14. The method of claim1, wherein the taxonomy signature from the sample is calibrated bycomparing the signature to a signature obtained from a reference samplethat is obtained away from the hydrocarbon seep.
 15. The method of claim14, further comprising: obtaining a second sample from an area notassociated with the hydrocarbon reservoir; extracting one or more ofproteins, lipids, or nucleic acids from the second sample; analyzing theextracted proteins, lipids, or nucleic acids from the second sample toidentify signatures that are indicative of organisms from theThermotogales order; identifying the relative abundance of differentgenera or species of Thermotogales present in the second sample andassigning a taxonomy signature to the second sample; comparing thetaxonomy signature of the second sample with the taxonomy signature ofthe sample taken from the hydrocarbon seep; using the compared taxonomysignature to determine the temperature of the hydrocarbon reservoir 16.The method of claim 14, wherein the reference sample is obtained at alocation that is at least 200 meters away from the center of thelocation where the seep is emanating from the surface.
 17. The method ofclaim 1, wherein the nucleic acid analysis comprises one or more of DNAanalysis, RNA analysis, and metagenomics.
 18. The method of claim 1,further comprising using the determined temperature to determine thedepth of the hydrocarbon reservoir in the subsurface.
 19. The method ofclaim 18, wherein determining the depth of the hydrocarbon reservoircomprises using a geothermal gradient to determine the depth from thedetermined temperature.
 20. The method of claim 18, further comprisingconducting a seismic survey of the hydrocarbon reservoir, wherein theseismic survey is targeted at the determined depth.
 21. The method ofclaim 18, further comprising using the determined depth to interpretseismic data of the hydrocarbon reservoir.